Second Beginnings
by Rrrfffggg1234
Summary: After three years at boarding school, 16 year old Clary Fray, must deal with her extremely mixed feelings about her brother's best friend Jace. Three years change a person, has it been for the better, or the worst?
1. Chapter 1: A New Start

**Hey guys! This is my first story on here so please feel free to leave any constructive criticism in the comments! It would really help me out. I hope you enjoy this story!**

***Disclaimer - I do not own any of these characters**

**August 20th, 2016 - New York Airport**

"I'm going to miss you so much sweetie!" Jocelyn, my mother, proclaimed as she gave me a strangling hug.

"I'll miss you too Mom." I normally wasn't the type to get mushy, especially not in a starch white airport terminal surrounded by strangers, but I began to feel the tears well up. I knew it was now or never. "Mom. Mom! I have to get on the plane. They're almost done boarding."

"Of course honey. I'm sorry." Jocelyn, average height for a woman, towered over my five foot two frame and wiped tears from her eyes. She was the type of person some would call 'soft', though she was the strongest woman I knew.

"Come here Clary." My brother Jon held his arms wide, a sad smile splayed on his lips. He scooped me up into the tightest hug he could muster. My head hit hard just under his shoulder, sending long red hair up to meet his short blond locks.

"Take care of her. I worry," I pleaded. I was going to the biggest art academy in the entire country. The only doubt that it was the right thing was the nagging knowledge that I was leaving my family behind.

"I will," he whispered. Now go catch your flight! People are starting to stare." I let out a giggle. We both knew that the last thing I cared about was what strangers thought. I was used to strange looks with my small stature and carrot-like hair.

"See you in three years!" I sped away, willing the water works to postpone their appearance. If my mom saw me crying, well, lets just say I wouldn't be going anywhere but back home.

**August 21, 2016 - Wayland Academy for the Highly Gifted Arts (WAFFLES)**

Wow. So I was really here. It had been my dream ever since I saw that ad on the school bulletin board in third grade. The Wayland Academy for the Highly Gifted Arts was the top high school in the nation. Only about 2% of all applicants get in. I always thought it was an impossible dream, but I started writing them immediately. I heard that the longer they watch you, the more likely you will be to get in, and I wanted to be noticed. I shook my head and reached into my pocket to pull out the directions to the main office. I started off only to stall a second later.

I screeched. "Oh! I'm so sorry!" Great. I ran into someone in my firs ten seconds of being on campus. Literally one of the only three people in sight. She turned and smiled. Annnnnd she's pretty. Of course, I, of all people have to bump into a probably popular girl on my first day. Way to make a good impression Fray.

"No worries. I'm Tessa. Are you new here?" I stopped. Her smile met her eyes. Maybe she was nice.

"Uh yeah. I'm Clary. Well, Clarissa. Clary, Clarissa, whatever." I sputtered "I was just looking for the main office." I spun in a slow circle, taking it all in for the first time. The gothic buildings had been given a fresh coat of gold and white paint to appear more modern. There was an old cathedral to the right, and a large line of buildings on the far left. I figured that must be where the classes are held.

"Oh! I can show you." She spun on her heel and took off down the hill. "So wait. What's your last name?" I wondered why it mattered, but thought better of asking.

"Fray."

"You just might be my new roomie! Here lets see." Her voice trailed off as she pulled a large paper from the top of her right Converse. It must be a California thing, cause I'd never seen anyone do that. "Yup! Right here, Clarisa Fray, room 232. They're coed this year though, so we'll also have two guys." She huffed, rolling her eyes.

I chuckled. "Well that worked out well." If I ran into anyone, I'm glad it was my roommate." Or maybe I wasn't.

**May 6th, 2019 - New York; Home**

I tipped the cabbie ten bucks and shut the door as quiet as possible. I paid extra money to make sure I got a new 'eco-friendly' car to reduce the noise. My mom would be mad she didn't get to pick me up, but I didn't tell her I was even coming home. I sighed and set down my luggage. Three years and the place looked no different. Same wood lined porch with the old white swing. The yellow paint my mom had forced on Luke looking bright as ever. I picked up my things and trudged up the steps. Due to a small dinning hall fire, school let out six days early. Since the school was 8-10th grade, they didn't need to worry about moving a graduation and just passed everyone.

I debated on whether or not to knock, before deciding against it and twisting the knob. "Knock knock," I shouted.

"Who in the world is in my house?" came a familiar voice from upstairs. "Jon is it one of your friends?" Jon rounded the corner from the living room and barely paused as he saw me.

"Clary!" He screamed, just before we collided. He had gotten stronger. A lot stronger.

"Let. Me. Breathe!" I panted as he let go. "So," I asked, regaining my composure. "How have you been?" His strength wasn't the only thing that had changed. He was 15 when I left. Now he was 17 and had filled into his features. He was taller now too, but so was I.

"How have I been? Clary it's been three years since I last saw you and all I get is a 'how have you been?" His face a mask of disbelief and apprehensiveness. It was like giving a child a puppy, and them being scared you were going to take it away. Before I could reply, Luke came barreling down the stairs.

"Did I hear Clary? I did!" He scooped me off my feet like I were a child. "Clary! I missed you so much." He set me down and stepped back, just a bit. He had a bit more grey in his stubble, but otherwise he hadn't changed.

"I missed you too. Is Mom here?" As excited as I was to see my stepfather, I really wanted to see my mom. His face dropped as soon as the words left my mouth.

"I'm sorry Clare. Your mother's away on business. I'm supposed to join her this evening, but I could stay home if you like?" While his voice sounded cheerful, his face told me it was not as simple as just 'staying home.'

"No! You should go. You and Mom go handle your business stuff and I'll get settled in." Truthfully, I didn't mind the idea. Jocelyn could sometimes be overbearing.

"Okay. I better finish packing then." He looked relieved as he jogged back upstairs, sparing one last glance in my direction. Whatever business situation was happening, it was certainly stressing him out.

"Okay," Oh no, "I've been sitting in the living room long enough. Now where's my hug?"


	2. Chapter 2: And the Feels Return

**September 23, 2016 - WAFFLES**

"Tessa, I have a question." Ever since my first day at school, Tessa and I had just gotten closer. I even met some of her friends. Aline, Helen, and Will were all really close, but somehow I had gotten into their group. "I have been here for a month, and no one has been able to tell me how you get WAFFLES from Wayland Academy for the Highly Gifted Arts."

"Oh," she giggled, "It doesn't really stand for anything. I think some jocks were drunk one night and decided that WAHGA sounds like a breakfast food." We were sitting at a round table in the commons with all our friends. Some shot Tessa a weird look, but it was Will who spoke up.

"That is," he stated, "precisely what happened." His ever present smirk turned into a smile when I looked at him.

"And just how would you know?" Will was only a year older than the rest of us. When I first saw him, I knew he looked familiar. Now I know why. Will Herondale was a spitting image of his cousin Jace Herondale, except for the hair and eyes. Will had dark black hair with blue eyes, where Jace had light golden blond hair and gold eyes. I sighed inwardly. Maybe all Herondales were just pretty

"I know, because I was one of those jocks, thank you very much." He didn't look like he was kidding, but Jace was always difficult to read too. As the year went on, it felt increasingly difficult to stop comparing Will and Jace.

**May 6th, 2019 - New York; Home**

"Okay," Oh no, "I've been sitting in the living room long enough. Now where's my hug?" It was Jace, my brother Jon's best friend since childhood. We had never been explicitly close, but we had started to hang out more right before I was accepted.

"Who says you get a hug?" I teased. "Maybe I'm all hugged out." If I thought he and Will looked similar before, now it was even more evident. His strong jawline and built body a perfect match to his cousin's. They were both painfully beautiful.

"Nope. Sorry carrot. I've been saving this hug for three years. Come here." I sighed and smiled. I didn't mind the hug, I just liked to tease Jace. His hug was more gentle than Jon's, but firm all the same. Just as he let me go, my phone started to ring.

"One second." I looked down, expecting to see my mom's number. Instead I saw Will's.

"Will? I wasn't expecting to hear from you so soon."

"Yeah, so about that. We have a problem." He sounded panicked.

"Will, what's going on?" This wasn't like him, he was normally one to get straight to the point.

"So my plane had a problem and we ended up in New York instead of London."

"How does that even happen?" So Will was in New York and calling me instead of his aunt. This outta be good.

"I have absolutely no clue. I think it was something about a weather turn around and too much air traffic, then low fuel. Anyway, I can't get ahold of my family so I was wondering if I could stop by your house?" Almost immediately I wanted to say yes, but I hesitated. Two Herondales in the same house? That has to be dangerous. "Clary? Is that okay?"

"Oh! Yeah! I'm sorry I just spaced out." He was already in a cab so I gave him my address and filled in Jon and Jace.

"So why is my cousin coming to your house?" Jace sounded perplexed and a bit mad? Surely he wasn't upset about seeing Will.

"We were pretty close in Cali." 'Pretty close' was an understatement. Will and I had dated for two and a half years at WAFFLES, and I was ecstatic that he would now get to see the home I had been going on and on about. "I've told him a lot about this place so I'm sure he probably wants to see it."

"I think it's a great idea," said Jon. "You get to see your cousin and Clary gets to see her boyfriend." Jon emphasized that last word and with a pointed look at Jace, he tensed.

Fifteen minutes later Will was at my door wearing a "New York, New York. So good they named it twice" hat and a black hoodie.

"Hey Clare," Will said as he pulled me into a hug. He kissed the top of my head before stepping back. "So this is your home? It's very pretty. It must be a New York thing." I smiled.

"Sorry to interrupt your reunion, but there's other people here too." Jace, obnoxious as always, stood impatiently at the foot of the stairs.

"Hey Jace." Will walked to him for a hug but Jace stepped back. They were never close due to the separation distance, but I had expected Jace to be more welcoming. Jon cleared his throat.

"So this is Will? I didn't expect him and Jace to look so similar." I always found it weird how close they looked. Maybe that was why I was so drawn to Will.

"Oh it gets weirder." Jace's voice was monotone as he stepped down from the last stair. "Will, can I talk to you?" Will hesitated. "Now." Jace stalked off into the living room, Will following close behind.

**Jace's POV **

For three years I held onto the belief that I would finally get to tell Clary how I felt. I considered the fact that she might have a few boyfriends from school, but never anyone I couldn't stack up to. Definitely never anything long term, and definitely never my cousin.

"Look. I don't know what you think you're doing here, but I think you should end things with Clary and go home." I bit my lip. I didn't want to stoop to begging, but I was willing to if needed.

"Excuse me?" Great. He was outraged. "I'm sorry. I must have heard you wrong. I didn't know you owned Clary." So, I might have messed up. Why did it have to be Will?

"Look. I'm just trying to look out for her," I lied. "You live all the way in London and she's only 16." I couldn't tell him the truth.

"If you must know, we broke up a few days ago. Though I don't see how that is any of your business." He was beyond mad. Will was showing no emotion on his face.

"I just care about her, that's all. Cousin to cousin, did you break up because of distance?" He looked at his feet, face flushed scarlet.

"I don't really wanna talk about it." He quickly shuffled from the room, regaining his composure.

"Did you find out anything else about your flight?" Clary asked. Will checked his phone, hand shaking.

"Yeah. It's rescheduled for tomorrow at 2 p.m. I guess I'll just try to find a hotel for the night." I let out a breathe I didn't know I was holding.

"Nonsense!" It was Jon. "We have an extra guest room you can stay in."

"Oh I couldn't. I wouldn't want to intrude on Clary's homecoming." I smirked. I didn't want him to stay.

"It's probably for the best-" I was cut off by Clary.

"No. Jon's right," she stated. "There's no use in you paying for a hotel when you can just stay here."

"Okay. Would it be alright if I headed up there now? I'd like to get a bit of rest."

"Yeah. Just follow me." Jon lead him up the stairs, neither glancing back.

Once they were completely out of sight, I turned to Clary. "What happened between you two?" She stiffened. It was definitely something big.

"I," she sighed. "It's a long story." I looked at my invisible watch.

"I have all the time you need Clarissa." Clary cringed. She hated being called by her full name.

"Don't call me that. Look, we just had a falling out. He and Tessa grew close, and we grew apart. That's all. No hard feelings." So that's what happened. I wanted to be mad, but it was I knew it was irrational.

"Oh. I didn't realize. I'm sorry Clary. You didn't deserve that." I wanted to console her more than was plausible.

"No it's okay. It had nothing to do with you." She looked at me, her beautiful green eyes filling with tears.

"Oh, but it did," I mumbled. I wanted to tell her, but now definitely wasn't the right time.

"What?"

"It's nothing."

**Thank you to all those who read, reviewed, followed, and favorited the first chapter! It's really motivating when I know others want to read it too! **

**Please continue to review and let me know if you think the chapters should be longer, or if you'd rather get a larger quantity of shorter ones like this one. **

**Thank You!**


	3. Chapter 3 : Settling In

**October 29, 2016 - Waffles Clary's P.O.V.**

"Tessa. I am NOT going to ask Will to homecoming." The last three days had just been her practically begging me to ask him. I was sure he would turn me down. Will was known for being a sort of player. He liked to go after the pretty girls who were basically a copy of their friends. Then when he was done, he'd move onto the next.

"Come on Clary. Please? I'm making you go anyways, so you might as well enjoy it."

"Who says I'd enjoy it if I went with Will?" Tessa knew I was stalling. The truth was, I liked Will. A lot.

"Clary, if you don't go ask him yourself, I will for you." She wasn't kidding. Tessa was exactly the type of friend who would do that. I sighed, about to respond when there was a knock at the door. "I got it." Tessa stood from her bed an eased open the door. "Speak of the devil."

"Hey Clary, can I talk to you?"

**May 6, 2019 - New York; Home - Jace's P.O.V.**

_No. Nope. Nada. This cannot be happening. _I couldn't believe I hurt Clary in anyway, indirect or otherwise. I tried to calm myself down by convincing me that I had no way of knowing he was dating Clary, but I just couldn't.

Looking into her eyes, it was almost if I could feel the immense pain she was in. I was just able to contain my tears until I got up to my room. I'd been staying with Jon for a while as me and Robert Lightwood weren't exactly on speaking terms. Luke and Jocelyn couldn't care less about Alec's sexual orientation, so we got along just fine.

I sighed and rolled so I was on my back. No sooner had I settled into place did I hear a quack. "DUCK!" I screamed, jumping to my feet. It sounded three more times before I realized the sound was coming from my phone, and Izzy was calling me. I made a mental note to change that ringtone.

"What ever could you want at 10 at night?" I swear, Izzy never went to bed.

"When were you going to tell me Clary was back in town?" Of course she called me about the last person I wanted to talk about.

"Look, I didn't think it was my place, okay? I really just wanna go to bed." I knew I was being harsh, but I wasn't about to break into tears while on the phone with Isabelle.

"Jace? What's wrong? Is it Clary?"

"No. Look, I'm going to bed. Goodnight Izzy." After a sigh of protest, she hung up.

**Two Weeks Later….. Clary's P.O.V**

I couldn't believe Izzy made me go out for the cheer squad. Not only that, but I actually made the squad. Though I'm sure Izzy, the caption, had something to do with that. We had been practicing for the last week and a half, even though it was early summer. We practiced on the football field since the boys had only started conditioning and not running drills. We were pretty good, easily mastering basic stunts and getting on to the fun stuff quickly. I'm not sure why they put the girl with the least experience, me, as center flyer, but they did, so I had to work twice as hard to learn everything I was behind on.

I had just executed the perfect side somi, when the football boys walked onto the field chanting "Throw her, throw her, throw her!" We all looked at each other knowing it was only light-hearted play.

"If you insist," Isabelle and three others prepared for a load in, "come on Clary." I stepped into place, smiling from ear to ear. She leaned down to whisper, "Be prepared for something high. We're gonna knock their socks off."

_1 2, _we shurgged, _3 4, they bent down ,5 6, I jumped in, 7 8, _and they threw me. Hard. We had to have set a record or something. I flew above the goal posts, before finally hitting the peak. I did a piked backflip, followed by a triple. The guys below shouted, alerting me that my efforts had not been in vain. The girls released me from their arms and I was swallowed by a mob of sweaty guys. In my short time back, I had made no shortage of friends.

**I know I said I wanted to make these longer, but I'm trying to develop background knowledge and characters before everything really starts to go down, so that's the main purpose of this chapter.**

**Please review, follow, and favorite! It's greatly appreciated!**


	4. Chapter 4: Who's Fault is It?

**Hey guys! I'm sorry for not updating, but it's been hectic with my school schedule and I just haven't been super inspired. I'd rather give fewer chapters I can be proud of than lots of uninspired rambles. **

**That being said, please ignore the weird football season timing, it's just gunna happen.**

**October 29, 2016 - WAFFLES; JcPenney**

"Blue or green?" It had only been a few hours since Will asked me to homecoming, and Tessa had already drug me out shopping. We were currently inside a JcPenney looking at their fanciest dresses.

"Definitely green!" Tessa reminded me of Izzy in only one way, she was a fashion expert. She knew exactly what color matches your skin and makes your eyes pop. She could tell you the most flattering cut of an item make you look your best. Izzy would have loved her.

"Are you sure it's not too, I don't know, REVEALING?" It was a skin tight, light green dress that ended just above mid-thigh. The neckline was a low V that showed a lot of skin.

"With the right makeup and accessories, no one will see the dress, just you. And no, it's not too revealing, I think Will is going to love it."

"That's not at all what I asked." I facepalmed. Of course Tessa would be thinking about what Will would want. I didn't mind the dress, but I'd rather go for something knee length with a high neckline. "Lets just go get shoes."

**October 30, 2016 - WAFFLES; Clary and Tessa's Room**

"Hurry up Tessa! The boys will be here soon." Tessa had been doing my hair and makeup for the past hour. She wouldn't let me do it myself, and she had gone all out.

"Oh shh Clary. You can't rush perfection! Trust me, when I get done you'll be glad you let me do this." I didn't let her do anything, and I made sure she knew it. "There I'm done." She walked me to our floor length mirror.

"Wow, I look, not like me." I laughed. I did look like me, but not exactly. My eyes shone and my hair sparkled. My cheekbones had never been more prominent. "I love it. Thank you."

"You're very welcome." Tessa beamed. Clary opened her mouth to speak, but was interrupted by a single loud knock on the door.

"Your dates have arrived." Sebastian and Will walked in without permission. Will joined me at the mirror. "You look, great. Really great."

"Thanks. You too." My efforts not to blush were in vain. "All ready to head out?" I was starving and our dinner reservations were in ten minutes.

**May 20, 2019 New York; School Parking Lot **

It was customary that after every football game, especially a win, all the students would meet in the school parking lot to party. Clary being a cheerleader was expected to attend, though she hated parties. Three hundred students all together drinking and vaping was not her idea of fun. Clary, Izzy, Jace, and Jon all attended regularly as a group.

"Iz, you should come dance with me," Jon called loudly over the music before leading her away. Neither of them had acknowledged it, but Clary had a sneaking suspicion there was something more going on with them. She made a mental note to ask Izzy later.

Clary glanced over the rim of her cup at Jace. He had been strangely distant since the moment Will came to her home. She hadn't talked to him about it yet, and figured now was as good of a time as ever.

"Jace?"

"Yeah Clary?"

"Can we talk? About Will?" Jace tensed.

"What's there to say? He's my cousin. I don't know him very well so if you're looking for ways to get with him again I can't help you." He turned away. The edge on his voice was palpable.

"That's not what I meant and you know it."

He sighed. "I'm just mad at myself okay?" His words trailed into a whisper, inaudible in the packed lot.

"Can we go somewhere else and talk. I'm ready to leave anyway." The four of us had taken two cars so we could leave at anytime.

"Okay," was all he said as he climbed into the driver's seat of his truck.

The house was empty when we arrived, as both Mom and Luke were away on business. Again. We joined each other in the living room to chat, sitting on opposite ends of the sofa.

I felt that being honest was the only way to get him to open up."I know there's something bothering you and it all started when Will came over. I can;t help but think this is my fault." Jace looked up, his expression shocked.

"Clary, none of this is your fault." He said it with such urgency I almost believed him.

"Then who's fault is it? I brought Will here and obviously you two don't get along well. I should have known."

"You couldn't have known. You couldn't have known anything." He looked at me with pity, not for me, but for himself. "Did you know he's coming for a visit?"

I did know. Will and I had been talking about it for months. Him and Tessa were coming up to see us and I couldn't wait to introduce them to my friends. "Yes I do know. I'm not sure it's the best idea though. I don't want you two to get mad at each other."

"Don't postpone seeing him because of me. I want you to be happy." He almost sounded sad. Like he was giving something up. "I'm going to bed now. I'll see you in the morning." With that, he stood up and left, leaving Clary alone with her thoughts.


	5. Chapter 5: Full of Firsts

**So I'm trying to incorporate some suggestions into the story about formatting. Mostly I will be trying to stick to the first section being her time at WAFFLES all taking place in a day or so and with any scene changes noted. The second half will be devoted to a 'current day' type form. As I have stated before these first few chapters are mostly about establishing some background info before things start to go down, which will be happening real soon. **

**Please follow, favorite, and review as it really helps to encourage me as an author seeing other people read my stories.**

**Hope you enjoy! **

**October 31, 2016 - WAFFLES **

"Thanks for the great day, Will" After the dance Will had asked me to go on a proper date with him the following Saturday. I promptly agreed. He took me to the biggest park in town, laying out a blanket and setting up the perfect picnic. We sat there and laughed for hours, learning about each other.

"I should be thanking you. Without you I would have no one to make fun of squirrels with." He smirked. Oh how I loved it when he smirked. We stood in silence.

"I guess I should go inside then…" I trailed off, not wanting to say goodbye.

"Clary," He bent his head down, meeting my lips. We broke apart as Tessa and Sebastian came down the hall.

**May 21, New York, Clary's House**

Clary didn't know how she'd ever slept in with the invasive sounds of the New York streets. Cars honking, people yelling, and trash clanking nonstop. The only sound at WAFFLES was Tessa's snoring. Waking up at 8 a.m. on a Saturday was unpleasant in itself, but waking up to find that she was alone with Jace made her stomach flip. Apparently everyone else had decided to get breakfast without altering either of them first.

"So what do you want for breakfast?" asked Jace. He'd been unusually nice to her since they talked last night.

"I'm going to make myself some eggs. Want any?" I walked over to get a pan. Luke must have put them on the top shelf while I was away, but now I couldn't reach them.

"Sit Clary." Jace grabbed the pan with ease and set it on the stove. He took my shoulders and guided me to the island stool. His touch lit up my skin. I shook away the thoughts. "Today I'm making breakfast."

I lacked the energy to fight him so instead, I sat watching. The way his muscles moved under his shirt. His graceful movements as he danced from the stove to the fridge and back again. I found myself wondering how it would be to wake up to this more often. I froze.

There's no way. I was not thinking about Jace Herondale, my brother's best friend and roommate, as if I _liked_ him. Nope. I must be dreaming. Having a nightmare to be exact.

"Ta Da!" I looked up to see Jace beaming down and a plate of fresh eggs and bacon sitting on the island. "I am certainly the best cook in the house. No offence to Jocelyn." I laughed. Jace could always make me laugh.

_Stop it Clary! _I could not think of Jace like this.

We finished eating with comfortable chatter and went our separate ways to get ready for the day.

By the time I got back downstairs, Jace was already sitting on the couch playing _Call of Duty._

"Hey Clary," Jace glanced up. "I'm just finishing up this match. It won't be long." He paused. "Unless you want to try?" If I didn't know better I'd think he sounded hopeful.

"Sure. If you want to teach me. I don't think I've picked up a controller since I left." That wasn't necessarily true. There was a time when Will and I played a lot of _Overwatch_.

"I'd love to. It's a shame. Your _Madden_ skills were unmatched." He choked down a laugh. I suck at _Madden._

"Hey!" I playfully thumped his head and sat down.

After he finished, he handed me the controller and quickly went over the basic movements. The explanation went right over my head.

By the end of the match we were both laughing to the point of tears. We had moved closer so Jace could help me with the controls, but somehow he ended with his arms around me. To my dismay, I found that I didn't mind.

"Clary," Jace stopped laughing. I turned toward him.

"Yeah?" He cupped my face and kissed me.


End file.
